Merge pull request #25 from alchem0x2A/singleio

Singleio

sparc/calculator.py

@@ -5,7 +5,7 @@
 import subprocess
 
 from .io import SparcBundle
-from .utils import _find_default_sparc, h2gpts
+from .utils import _find_default_sparc, h2gpts, deprecated
 from warnings import warn, warn_explicit
 from .api import SparcAPI
 import datetime
@@ -27,22 +27,6 @@
 defaultAPI = SparcAPI()
 
 
-def deprecated(message):
-    def decorator(func):
-        def new_func(*args, **kwargs):
-            warn(
-                "Function {} is deprecated sparc-dft-api >= v0.2! {}".format(
-                    func.__name__, message
-                ),
-                category=DeprecationWarning,
-            )
-            return func(*args, **kwargs)
-
-        return new_func
-
-    return decorator
-
-
 class SPARC(FileIOCalculator):
     # TODO: magmom should be a possible input
     implemented_properties = ["energy", "forces", "fermi", "stress"]

sparc/io.py

@@ -27,7 +27,7 @@
 from .sparc_parsers.pseudopotential import copy_psp_file, parse_psp8_header
 from .common import psp_dir as default_psp_dir
 from .download_data import is_psp_download_complete
-from .utils import string2index
+from .utils import string2index, deprecated
 
 from ase.calculators.singlepoint import SinglePointDFTCalculator
 from ase.units import Hartree
@@ -671,6 +671,61 @@ def write_sparc(filename, images, **kwargs):
     return
 
 
+@deprecated("Reading individual .ion is not recommended. Please use read_sparc instead.")
+def read_ion(filename, **kwargs):
+    """Parse an .ion file inside the SPARC bundle using a wrapper around SparcBundle
+    The reader works only when other files (.inpt) exist.
+
+    The returned Atoms object of read_ion method only contains the initial positions
+    """
+    parent_dir = Path(filename).parent
+    sb = SparcBundle(directory=parent_dir)
+    atoms = sb._read_ion_and_inpt()
+    return atoms
+
+@deprecated("Writing individual .ion file is not recommended. Please use write_sparc instead.")
+def write_ion(filename, atoms, **kwargs):
+    """Write .ion and .inpt files using the SparcBundle wrapper.
+
+    This is only for backward compatibility
+    """
+    label = Path(filename).with_suffix("").name
+    parent_dir = Path(filename).parent
+    sb = SparcBundle(directory=parent_dir, label=label)
+    sb._write_ion_and_inpt(atoms, **kwargs)
+    return atoms
+
+
+def read_static(filename, index=-1, **kwargs):
+    """Parse a .static file bundle using a wrapper around SparcBundle
+    The reader works only when other files (.ion, .inpt) exist.
+    """
+    parent_dir = Path(filename).parent
+    sb = SparcBundle(directory=parent_dir)
+    atoms_or_images = sb.convert_to_ase(index=index, **kwargs)
+    return atoms_or_images
+
+
+def read_geopt(filename, index=-1, **kwargs):
+    """Parse a .geopt file bundle using a wrapper around SparcBundle
+    The reader works only when other files (.ion, .inpt) exist.
+    """
+    parent_dir = Path(filename).parent
+    sb = SparcBundle(directory=parent_dir)
+    atoms_or_images = sb.convert_to_ase(index=index, **kwargs)
+    return atoms_or_images
+
+
+def read_aimd(filename, index=-1, **kwargs):
+    """Parse a .static file bundle using a wrapper around SparcBundle
+    The reader works only when other files (.ion, .inpt) exist.
+    """
+    parent_dir = Path(filename).parent
+    sb = SparcBundle(directory=parent_dir)
+    atoms_or_images = sb.convert_to_ase(index=index, **kwargs)
+    return atoms_or_images
+
+
 def register_ase_io_sparc(name="sparc"):
     """
     Monkey patching the ase.io and ase.io.formats
@@ -772,6 +827,29 @@ def _new_filetype(filename, read=True, guess=True):
                     "Atomatic format inference for sparc is not correctly registered. "
                     "You may need to use format=sparc in ase.io.read and ase.io.write. "
                 )
+    # Add additional formats including .ion (r/w), .static, .geopt, .aimd
+    F(
+        "ion",
+        desc="SPARC .ion file",
+        module="sparc",
+        code="1S",
+        ext="ion",
+    )
+    F(
+        "static",
+        desc="SPARC single point results",
+        module="sparc",
+        code="+S",
+        ext="static",
+    )
+    F(
+        "geopt",
+        desc="SPARC geometric optimization results",
+        module="sparc",
+        code="+S",
+        ext="geopt",
+    )
+    F("aimd", desc="SPARC AIMD results", module="sparc", code="+S", ext="aimd")
 
     # TODO: remove print options as it may be redundant
-    print("Successfully registered sparc format with ase.io!")
+    print("Successfully registered sparc formats with ase.io!")

sparc/utils.py

@@ -3,9 +3,26 @@
 import os
 import shutil
 import numpy as np
+from warnings import warn
 from typing import Union, List, Optional
 
 
+def deprecated(message):
+    def decorator(func):
+        def new_func(*args, **kwargs):
+            warn(
+                "Function {} is deprecated sparc-dft-api >= v0.2! {}".format(
+                    func.__name__, message
+                ),
+                category=DeprecationWarning,
+            )
+            return func(*args, **kwargs)
+
+        return new_func
+
+    return decorator
+
+
 def string2index(string: str) -> Union[int, slice, str]:
     """Convert index string to either int or slice
     This method is a copy of ase.io.formats.string2index

tests/test_000_ase_io.py

@@ -178,9 +178,31 @@ def fake_read_sparc(filename, *args, **kwargs):
     assert atoms.get_chemical_formula() == "Al"
 
 
-def test_ase_io_filetype():
-    """If hacked ase.io.formats.filetype correctly recognized sparc format"""
+def test_ase_io_filetype(fs):
+    """If hacked ase.io.formats.filetype correctly recognized sparc format
+
+    Due to the implementation of ase.io.formats, single file tests should be
+    done on non-empty files
+    """
     import sparc
     from ase.io.formats import filetype
 
+    fs.create_dir("test.sparc")
+    fs.create_file("test.sparc/test.ion")
+    fs.create_file("test.sparc/test.static")
+    fs.create_file("test.sparc/test.geopt")
+    fs.create_file("test.sparc/test.aimd")
+    with open("test.sparc/test.ion", "w") as fd:
+        fd.write("\n")
+    with open("test.sparc/test.static", "w") as fd:
+        fd.write("\n")
+    with open("test.sparc/test.geopt", "w") as fd:
+        fd.write("\n")
+    with open("test.sparc/test.aimd", "w") as fd:
+        fd.write("\n")
+
     assert filetype("test.sparc") == "sparc"
+    assert filetype("test.sparc/test.ion") == "ion"
+    assert filetype("test.sparc/test.static") == "static"
+    assert filetype("test.sparc/test.geopt") == "geopt"
+    assert filetype("test.sparc/test.aimd") == "aimd"